I am a PhD candidate in Computer Science at Princeton University. I am very fortunate to be advised by Ben Raphael. Prior to working with Ben Raphael, I completed a Bachelor of Science in Math and Computer Science at Tufts University, where I worked with Lenore Cowen designing algorithms for protein-to-protein interaction networks.
Currently, my research employs techniques from theoretical computer science and operations research to study problems in computational biology. Specifically, I apply these techniques to study phylogenetic optimization problems that arise in cancer evolution and lineage tracing. As an example, my recent work fastBE develops specialized algorithms to enable large-scale phylogenetic reconstruction of tumors using primal-dual methods for solving linear programs.
Recent Updates
- (January 2025) Our preprint Fast tumor phylogeny regression via tree-structured dual dynamic programming is now available on bioRxiv.
- (December 2024) The tree labeling polytope manuscript was accepted for presentation at RECOMB2025.
- (December 2024) The fastBE manuscript was published in PLoS Computational Biology.
- (September 2024) Attended the ICERM workshop regarding Current Methods and Open Problems in Mathematical and Statistical Phylogenetics.
- (April 2024) The fastBE paper was presented at RECOMB-CCB.
Journal Publications
* denotes joint first authorship; author order is rearranged with permission from co-authors.
Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
Henri Schmidt*, Minsi Zhang*, Haralambos Mourelatos, Francisco J. Sánchez-Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin
Genome Biology, Volume 26, Article 41, February 26, 2025.
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
Henri Schmidt, Benjamin J. Raphael
PLoS Computational Biology, Volume 20, Issue 12, December 2024. [slides]
Multi-center integrated analysis of non-coding CRISPR screens
David Yao, Josh Tycko, …, Henri Schmidt, …, Michael C. Bassik, Steven K. Reilly
Nature Methods, Volume 21, Issue 4, Pages 723-734, February 2024.
Startle: A star homoplasy approach for CRISPR-Cas9 Lineage Tracing
Henri Schmidt*, Palash Sashittal*, Michelle Chan, Benjamin J. Raphael
Cell Systems, Volume 14, Issue 12, December 2023, Pages 1113-1121. [slides]
A zero agnostic model for copy number evolution in cancer
Henri Schmidt, Palash Sashittal, Benjamin J. Raphael
PLoS Computational Biology, Volume 19, Issue 11, November 2023. [slides]
GLIDER: function prediction from GLIDE-based neighborhoods
Kapil Devkota, Henri Schmidt, Matt Werenski, James M Murphy, Mert Erden, Victor Arsenescu, Lenore J Cowen
Bioinformatics, Volume 38, Issue 13, July 2022, Pages 3395-3406.
Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants
Francisco J Sánchez-Rivera, Bianca J Diaz, Edward R Kastenhuber, Henri Schmidt, …, Scott W. Lowe, Lukas Dow
Nature biotechnology, Volume 40, Issue 6, June 2022, Pages 862-873.
Preprints
The tree labeling polytope: a unified approach to ancestral reconstruction problems
Henri Schmidt, Benjamin J. Raphael
bioRxiv, February 19th, 2025. Presenting at RECOMB 2025.
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Henri Schmidt*, Yuanyuan Qi*, Benjamin J. Raphael, Mohammed El-Kebir
bioRxiv, January 27th, 2025.
Inferring cell differentiation maps from lineage tracing data
Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Alexander Strzalkowski, Henri Schmidt, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael
bioRxiv, September 13th, 2024.